Ontology type: schema:ScholarlyArticle
2009-07
AUTHORSPrateek Kumar, Steven Henikoff, Pauline C Ng
ABSTRACTThe effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5-20 min, depending on the input. SIFT is available as an online tool (http://sift.jcvi.org). More... »
PAGES1073-1081
http://scigraph.springernature.com/pub.10.1038/nprot.2009.86
DOIhttp://dx.doi.org/10.1038/nprot.2009.86
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1015642657
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/19561590
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Algorithms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Amino Acid Sequence",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Amino Acid Substitution",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Computer Simulation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Internet",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Molecular Sequence Data",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Phenotype",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Proteins",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Software",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "J. Craig Venter Institute",
"id": "https://www.grid.ac/institutes/grid.469946.0",
"name": [
"Department of Genomic Medicine, J. Craig Venter Institute, San Diego, California, USA."
],
"type": "Organization"
},
"familyName": "Kumar",
"givenName": "Prateek",
"id": "sg:person.0720326117.36",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0720326117.36"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Fred Hutchinson Cancer Research Center",
"id": "https://www.grid.ac/institutes/grid.270240.3",
"name": [
"Basic Sciences Division, Howard Hughes Medical Institute, Seattle, Washington, USA.",
"Fred Hutchinson Cancer Research Center, Seattle, Washington, USA."
],
"type": "Organization"
},
"familyName": "Henikoff",
"givenName": "Steven",
"id": "sg:person.01110332674.32",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110332674.32"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Fred Hutchinson Cancer Research Center",
"id": "https://www.grid.ac/institutes/grid.270240.3",
"name": [
"Department of Genomic Medicine, J. Craig Venter Institute, San Diego, California, USA.",
"Fred Hutchinson Cancer Research Center, Seattle, Washington, USA."
],
"type": "Organization"
},
"familyName": "Ng",
"givenName": "Pauline C",
"id": "sg:person.011056174642.58",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011056174642.58"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1101/gr.212802",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001576197"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkg509",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002198958"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/(sici)1098-1004(200001)15:1<45::aid-humu10>3.0.co;2-t",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003133387"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2105-7-166",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008763878",
"https://doi.org/10.1186/1471-2105-7-166"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/10290",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008973203",
"https://doi.org/10.1038/10290"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/10290",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008973203",
"https://doi.org/10.1038/10290"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.176601",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014452737"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1373/clinchem.2004.036053",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026189507"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.772403",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030905286"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev.genom.7.080505.115630",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033519727"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0022-2836(02)00813-6",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033884262"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1046/j.1523-1747.1999.00554.x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1035976237",
"https://doi.org/10.1046/j.1523-1747.1999.00554.x"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.3804205",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036448879"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkj518",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042952078"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkf493",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043756780"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/bti486",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046984261"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/25.17.3389",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047265454"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev.arplant.54.031902.135009",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047671775"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1086/302711",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1058610277"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1089/gte.1997.1.237",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1059267014"
],
"type": "CreativeWork"
}
],
"datePublished": "2009-07",
"datePublishedReg": "2009-07-01",
"description": "The effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5-20 min, depending on the input. SIFT is available as an online tool (http://sift.jcvi.org).",
"genre": "research_article",
"id": "sg:pub.10.1038/nprot.2009.86",
"inLanguage": [
"en"
],
"isAccessibleForFree": false,
"isFundedItemOf": [
{
"id": "sg:grant.2529321",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1037502",
"issn": [
"1754-2189",
"1750-2799"
],
"name": "Nature Protocols",
"type": "Periodical"
},
{
"issueNumber": "7",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "4"
}
],
"name": "Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm",
"pagination": "1073-1081",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"4a87725f9bceb9f860d6f9d0bbf088593b8cfa08ccff1bee005ce6c80fe7f71b"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"19561590"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101284307"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/nprot.2009.86"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1015642657"
]
}
],
"sameAs": [
"https://doi.org/10.1038/nprot.2009.86",
"https://app.dimensions.ai/details/publication/pub.1015642657"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T22:19",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8690_00000422.jsonl",
"type": "ScholarlyArticle",
"url": "http://www.nature.com/articles/nprot.2009.86"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nprot.2009.86'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nprot.2009.86'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nprot.2009.86'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nprot.2009.86'
This table displays all metadata directly associated to this object as RDF triples.
186 TRIPLES
21 PREDICATES
57 URIs
30 LITERALS
18 BLANK NODES